Data Acquisition and Conversion

Overview

MR spectroscopy data is initially exported from the scanner as .rda files. However, LCModel requires data in .RAW format. Converting from .rda to .RAW involves more than simply renaming the file—it requires reading the data and writing it out in a compatible format.

Procedure

1. Data Export Export your raw spectroscopy data from the scanner, typically saved in the .rda format.

2. Conversion with FID-A Toolbox (MATLAB) Use the FID-A toolbox to load and convert the files. The following MATLAB script demonstrates the process:

   % Add FID-A to MATLAB path
   addpath(genpath('/Users/SH7437/FID-A-master'));
   
   % Load the RDA files for suppressed and unsuppressed acquisitions
   in_suppressed = io_loadspec_rda('/Users/SH7437/Desktop/suppressed.rda');
   in_unsuppressed = io_loadspec_rda('/Users/SH7437/Desktop/unsuppressed.rda');
   
   % Set the echo time (TE) in milliseconds (update as needed)
   TE = 30;
   
   % Write out .RAW files for LCModel usage
   io_writelcm(in_suppressed, '/Users/SH7437/Desktop/suppressed.raw', TE);
   io_writelcm(in_unsuppressed, '/Users/SH7437/Desktop/unsuppressed.raw', TE);
   

Key Points

• The function io_loadspec_rda reads the RDA file.

• The function io_writelcm writes the data into the .RAW format needed by LCModel.

• Adjust the TE (echo time) as per your experimental settings. - Example: Glutamate/Glutamine → neurotransmitter function.

Raw Phantom Data

• Suppressed Phantom Data

• Unsuppressed Phantom Data

LCModel Manual

This is the official LCModel manual.

Download LCModel Manual (PDF)